Vector AutoRegressive Moving Average Models: A Review.

Vector AutoRegressive Moving Average (VARMA) models form a powerful and general model class for analyzing dynamics among multiple time series. While VARMA models encompass the Vector AutoRegressive (VAR) models, their popularity in empirical applications is dominated by the latter. Can this phenomenon be explained fully by the simplicity of VAR models? Perhaps many users of VAR models have not fully appreciated what VARMA models can provide.

Classifying contaminated cell cultures using time series features.

We examine the use of time series data, derived from Electric Cell-substrate Impedance Sensing (ECIS), to differentiate between standard mammalian cell cultures and those infected with a mycoplasma organism. With the goal of easy visualization and interpretation, we perform low-dimensional feature-based classification, extracting application-relevant features from the ECIS time courses. We can achieve very high classification accuracy using only two features, which depend on the cell line under examination.

Generating a multimodal artificial intelligence model to differentiate benign and malignant follicular neoplasms of the thyroid: A proof-of-concept study.

Background: Machine learning has been increasingly used to develop algorithms that can improve medical diagnostics and prognostication and has shown promise in improving the classification of thyroid ultrasound images. This proof-of-concept study aims to develop a multimodal machine-learning model to classify follicular carcinoma from adenoma.

Methods: This is a retrospective study of patients with follicular adenoma or carcinoma at a single institution between 2010 and 2022.

Addressing the Embeddability Problem in Transition Rate Estimation.

Markov State Models (MSM) and related techniques have gained significant traction as a tool for analyzing and guiding molecular dynamics (MD) simulations due to their ability to extract structural, thermodynamic, and kinetic information on proteins using computationally feasible MD simulations. The MSM analysis often relies on spectral decomposition of empirically generated transition matrices. This work discusses an alternative approach for extracting the thermodynamic and kinetic information from the so-called rate/generator matrix rather than the transition matrix.

Group linear non-Gaussian component analysis with applications to neuroimaging.

Independent component analysis (ICA) is an unsupervised learning method popular in functional magnetic resonance imaging (fMRI). Group ICA has been used to search for biomarkers in neurological disorders including autism spectrum disorder and dementia. However, current methods use a principal component analysis (PCA) step that may remove low-variance features.

Exploring Blob Detection to Determine Atomic Column Positions and Intensities in Time-Resolved TEM Images with Ultra-Low Signal-to-Noise.

Spatially resolved in situ transmission electron microscopy (TEM), equipped with direct electron detection systems, is a suitable technique to record information about the atom-scale dynamics with millisecond temporal resolution from materials. However, characterizing dynamics or fluxional behavior requires processing short time exposure images which usually have severely degraded signal-to-noise ratios. The poor signal-to-noise associated with high temporal resolution makes it challenging to determine the position and intensity of atomic columns in materials undergoing structural dynamics.

Multivariate random forest prediction of poverty and malnutrition prevalence.

Advances in remote sensing and machine learning enable increasingly accurate, inexpensive, and timely estimation of poverty and malnutrition indicators to guide development and humanitarian agencies' programming. However, state of the art models often rely on proprietary data and/or deep or transfer learning methods whose underlying mechanics may be challenging to interpret. We demonstrate how interpretable random forest models can produce estimates of a set of (potentially correlated) malnutrition and poverty prevalence measures using free, open access, regularly updated, georeferenced data.

Critical Risk Indicators (CRIs) for the electric power grid: a survey and discussion of interconnected effects.

The electric power grid is a critical societal resource connecting multiple infrastructural domains such as agriculture, transportation, and manufacturing. The electrical grid as an infrastructure is shaped by human activity and public policy in terms of demand and supply requirements. Further, the grid is subject to changes and stresses due to diverse factors including solar weather, climate, hydrology, and ecology.

AURORA: A Unified fRamework fOR Anomaly detection on multivariate time series.

The ability to accurately and consistently discover anomalies in time series is important in many applications. Fields such as finance (fraud detection), information security (intrusion detection), healthcare, and others all benefit from anomaly detection. Intuitively, anomalies in time series are time points or sequences of time points that deviate from normal behavior characterized by periodic oscillations and long-term trends.

Cell Line Classification Using Electric Cell-Substrate Impedance Sensing (ECIS).

We present new methods for cell line classification using multivariate time series bioimpedance data obtained from electric cell-substrate impedance sensing (ECIS) technology. The ECIS technology, which monitors the attachment and spreading of mammalian cells in real time through the collection of electrical impedance data, has historically been used to study one cell line at a time. However, we show that if applied to data from multiple cell lines, ECIS can be used to classify unknown or potentially mislabeled cells, factors which have previously been associated with the reproducibility crisis in the biological literature.

An unusual cause of shoulder pain and weakness.

Shoulder pain and weakness are common presenting Emergency Department complaints. Patients are often diagnosed with fractures, dislocations, bursitis, and muscle strain. Here we present an unusual cause of shoulder pain in an athletic and otherwise healthy young patient that does not respond to typical treatments for musculoskeletal pain.

Spatiotemporal mixed modeling of multi-subject task fMRI via method of moments.

Estimating spatiotemporal models for multi-subject fMRI is computationally challenging. We propose a mixed model for localization studies with spatial random effects and time-series errors. We develop method-of-moment estimators that leverage population and spatial information and are scalable to massive datasets.

An evaluation of independent component analyses with an application to resting-state fMRI.

We examine differences between independent component analyses (ICAs) arising from different assumptions, measures of dependence, and starting points of the algorithms. ICA is a popular method with diverse applications including artifact removal in electrophysiology data, feature extraction in microarray data, and identifying brain networks in functional magnetic resonance imaging (fMRI). ICA can be viewed as a generalization of principal component analysis (PCA) that takes into account higher-order cross-correlations.

Boronic esters in asymmetric synthesis.

The author's work on (α-haloalkyl)boronic esters as reagents for asymmetric synthesis is reviewed. Diastereomeric ratios exceeding 1000 can be achieved with this chemistry, and ratios around 100 are commonplace. The method allows sequential installation of a series of stereocenters and tolerates a wide variety of suitably protected functional substituents.

Synthesis and properties of 1-(3'-dihydroxyboryl-2',3'-dideoxyribosyl)pyrimidines.

Nucleoside analogues having a boronic acid in place of the 3-hydroxyl group of deoxyribose have been synthesized. The synthesis of 3'-dihydroxyboryl-2',3'-dideoxyribose was based on asymmetric homologation of boronic esters with (dihalomethyl)lithium, beginning from a (silyloxymethyl)boronic ester. A change of chiral director is required before introduction of the second stereocenter, and the direct displacement of (S,S)-1,2-dicyclohexyl-1,2-ethanediol by (1S,2S,3R,5S)-pinanediol was used for this purpose.

Knockout of Na+/Ca2+ exchanger in smooth muscle attenuates vasoconstriction and L-type Ca2+ channel current and lowers blood pressure.

Mice with smooth muscle (SM)-specific knockout of Na(+)/Ca(2+) exchanger type-1 (NCX1(SM-/-)) and the NCX inhibitor, SEA0400, were used to study the physiological role of NCX1 in mouse mesenteric arteries. NCX1 protein expression was greatly reduced in arteries from NCX1(SM-/-) mice generated with Cre recombinase. Mean blood pressure (BP) was 6-10 mmHg lower in NCX1(SM-/-) mice than in wild-type (WT) controls.

Activation of L-type Ca2+ channels by protein kinase C is reduced in smooth muscle-specific Na+/Ca2+ exchanger knockout mice.

L-type voltage-gated Ca(2+) channels (LVGCs) are functionally downregulated in arterial smooth muscle (SM) cells (ASMCs) of mice with SM-specific knockout of Na(+)/Ca(2+) exchanger type-1 (NCX1(SM-/-)) (32). Here, using activators and inhibitors of protein kinase C (PKC), we explore the regulation of these channels by a PKC-dependent mechanism. In both wild-type (WT) and NCX1(SM-/-) myocytes, the PKC activator phorbol 12,13-dibutyrate (PDBu) increases LVGC conductance, decreases channel closing rate, and shifts the voltage dependence of channel opening to more negative potentials.

Late phase TNF-alpha depression in natural orifice translumenal endoscopic surgery (NOTES) peritoneoscopy.

Background: Natural orifice translumenal endoscopic surgery (NOTES) allows access to the peritoneal cavity without skin incisions. Contamination of the peritoneal cavity by enteric contents may render NOTES more physiologically and immunologically invasive than previously thought. Measurement of interleukin-1 (IL-1), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-alpha) is a validated method to quantify surgical stress.

alpha-Amido boronic acids: a synthetic challenge and their properties as serine protease inhibitors.

This review includes a personal account of the history of the development of the alpha-amido boronic acid synthesis and related chemistry in the author's laboratory, as well as a review of some of the more significant developments that have occurred elsewhere more recently. The simple initial target, suggested by biochemist G. E.

Role of Cav1.2 L-type Ca2+ channels in vascular tone: effects of nifedipine and Mg2+.

Ca(2+) entry via L-type voltage-gated Ca(2+) channels (LVGCs) is a key factor in generating myogenic tone (MT), as dihydropyridines (DHPs) and other LVGC blockers, including Mg(2+), markedly reduce MT. Recent reports suggest, however, that elevated external Mg(2+) concentration and DHPs may also inhibit other Ca(2+)-entry pathways. Here, we explore the contribution of LVGCs to MT in intact, pressurized mesenteric small arteries using mutant mice (DHP(R/R)) expressing functional but DHP-insensitive Ca(v)1.

Bacterial birth scar proteins mark future flagellum assembly site.

Many prokaryotic protein complexes underlie polar asymmetry. In Caulobacter crescentus, a flagellum is built exclusively at the pole that arose from the previous cell division. The basis for this pole specificity is unclear but could involve a cytokinetic birth scar that marks the newborn pole as the flagellum assembly site.

Sodium pump alpha2 subunits control myogenic tone and blood pressure in mice.

A key question in hypertension is: How is long-term blood pressure controlled? A clue is that chronic salt retention elevates an endogenous ouabain-like compound (EOLC) and induces salt-dependent hypertension mediated by Na(+)/Ca(2)(+) exchange (NCX). The precise mechanism, however, is unresolved. Here we study blood pressure and isolated small arteries of mice with reduced expression of Na(+) pump alpha1 (alpha1(+/-)) or alpha2 (alpha2(+/-)) catalytic subunits.